Recurrent benign copy number variants & issues in interpretation of variants of unknown significance identified by cytogenetic microarray in Indian patients with intellectual disability.

BACKGROUND & OBJECTIVES: Cytogenetic microarray (CMA) is now recommended as a first-tier clinical diagnostic test in cases with idiopathic intellectual disability and/or developmental delay (ID/DD). Along with clinically relevant variants, CMA platforms also identify variants of unknown significance (VUS). This study was done to look for utility and various issues in interpretation of copy number variants (CNVs) in Indian patients with ID/DD. METHODS: The CMA was performed in 86 Indian patients with idiopathic ID/DD with or without dysmorphic features. CNV was reported if copy number gain was >400 kb in size and copy number loss was > 200 kb in size. RESULTS: Pathogenic CNVs were found in 18 of 86 (20.9%) patients. One large (14 Mb size) de novo heterozygous copy number gain was found in one patient. VUS (total 31) were present in 17 of 86 (19.7%) patients. Five novel recurrent benign CNVs were also present in our patients. INTERPRETATION & CONCLUSIONS: Our findings highlight the difficulties in interpretation of CNVs identified by CMA. More Indian data on VUS and recurrent benign CNVs will be helpful in the interpretation of CMA in patients with ID/DD.

A syndrome of facial dysmorphism, cubital pterygium, short distal phalanges, swan neck deformity of fingers, and scoliosis.

We report on an adolescent girl with sparse scalp hair, wide columella extending below alae nasi, webbing at elbows, broad finger tips, short distal phalanx of fingers, swan neck deformity of fingers, scoliosis, tall vertebrae, short fibulae, short fourth metatarsal bone, abnormal distal humeri, and unilateral clubfoot at birth. The combination of these features represents a novel phenotype. We sequenced the protein-coding regions of the FLNA and FLNB genes and did not observe any pathogenic sequence variation. Chromosomal microarray revealed a de novo copy number variation of uncertain clinical significance on 7p22.3.

Brothers with hypospadias, vertebral segmentation defects, and intellectual disability: new syndrome?

We report on two brothers (born to nonconsanguineous parents) with short stature, hypospadias, scoliosis, vertebral segmentation defects of "spondylocostal dysostosis" type, and intellectual disability. Results of cytogenetic and molecular genetic tests performed, including routine karyotype, MLPA (multiplex ligation-dependent probe amplification) for common microdeletions and subtelomeric copy number variants, microarray-CGH analysis, and sequencing of four Notch signaling pathway genes (DLL3, MESP2, LFNG, and HES7), were all normal. We present a comparison of the condition in the two boys with known syndromes and suggest that they may represent a hitherto unreported syndrome, most likely following autosomal recessive inheritance, though X-linked inheritance is not excluded.

Amplified fragment length polymorphism (AFLP) analysis is useful for distinguishing Leishmania species of visceral and cutaneous forms.

The Leishmania strains belonging to cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL) have been reported to possess close homology in genome profiles. To confirm this on genetic basis an attempt was made to differentiate Leishmania major; Leishmania tropica and Leishmania donovani genetically for the first time using amplified fragment length polymorphism (AFLP)--a high throughput DNA fingerprinting technique. The objective of this research work was to identify DNA markers of CL and VL. Ten combinations of selective primers detect a total of 1487 informative AFLP marker. Percentage of polymorphism was 45.12%. Three hundred and thirty-seven unique AFLP markers were also identified in three species of Leishmania. A clear distinction was revealed between L. major and L. donovani. It was inferred by AFLP analysis that a higher rate of polymorphisms occurred among Leishmania species which indicate the distinguished pattern of the disease cause by Leishmania, i.e. VL and CL. Analysis based on polymorphic AFLP markers revealed considerably high genetic variation among the genome of these species which was sufficient to distinguish between CL and VL.

Identification of genetic markers in sodium antimony gluconate (SAG) sensitive and resistant Indian clinical isolates of Leishmania donovani through amplified fragment length polymorphism (AFLP).

Sodium Antimony Gluconate (SAG) is currently used worldwide as the first-line drugs for the treatment of visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL) since 1940s. Unfortunately, the resistance of Leishmania parasite to this drug is increasing in several parts of the world. The mechanism of drug resistance in clinical isolates is still not very clear. Earlier, we have established a differentiation between six clinical isolates as sensitive and resistant on the basis of their sensitivity to SAG in vitro and in vivo as well as expression of proteophosphoglycan contents. In this preliminary study, we have further analyzed these isolates on the basis of their genetic diversity, molecular variance and phylogenetic structure using for the first time, a fingerprinting approach--amplified fragment length polymorphism (AFLP). Altogether 2338 informative AFLP bands were generated using 10 selective primer combinations. Percentage of polymorphism was 55.35%. A number of unique AFLP markers (217) were also identified in these strains. It was deduced that a higher rate of variations occurred among Leishmania clinical isolates which indicate the shifting of drug sensitive nature of parasite towards resistant condition.